Clustering

This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.

Set Up

# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)

# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")

# Source custom functions script
source(file.path("utils", "clustering-functions.R"))

Read in data

sample_290_normalized <- read_rds(
  file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))

Perform clustering

k-means

# Perform k-means clustering
kmeans_cluster_names <- paste("kmeans", c(2:5), sep = "_")

sample_290_normalized <- kmeans_clustering(
  sample_290_normalized,
  k_range = c(2:5),
  check_stability = TRUE
)

# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
  purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))

cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)

graph-based, walktrap

# Perform graph-based walktrap clustering
walktrap_cluster_names <-paste("walktrap", c(5, 10, 15, 20, 25), sep = "_")

sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  nn_range = c(5, 10, 15, 20, 25),
  weighting_type = "rank",
  cluster_function = "walktrap",
  check_stability = TRUE
)

Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'

# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))

cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)

graph-based, louvain

# Perform graph-based louvain clustering
louvain_cluster_names <- paste("louvain", c(5, 10, 15, 20, 25), sep = "_")

sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  nn_range = c(5, 10, 15, 20, 25),
  weighting_type = "jaccard",
  cluster_function = "louvain",
  check_stability = TRUE
)

Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'

# Plot
louvain_plot_list <- louvain_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))


cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)

Check cluster validity stats

k-means

# Check the k-means cluster validity stats for each of the clusters and produce
# a summary data frame of these stats to be stored within the SCE object
kmeans_stats_df <- add_metadata_clustering_stats(sample_290_normalized, c(2:5), "kmeans")

Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"

# Preview the results
head(kmeans_stats_df)

# Summarize the stats
kmeans_summary_stats_df <- summarize_clustering_stats(kmeans_stats_df)

# Preview the summary results
head(kmeans_summary_stats_df)

purity plots

# Plot individual cluster and summary stats
kmeans_purity_plots <- plot_clustering_validity(kmeans_stats_df, "purity", "maximum", "cluster_names", "purity")

kmeans_purity_plots

silhouette width plots

# Plot individual cluster and summary stats
kmeans_silhouette_plots <- plot_clustering_validity(kmeans_stats_df, "width",
                                                    "closest", "cluster_names", "silhouette")
kmeans_silhouette_plots

graph-based, walktrap

# Check the walktrap cluster validity stats for each of the clusters and return

purity plots

# Plot individual cluster and summary stats
walktrap_purity_plots <- plot_clustering_validity(walktrap_stats_df,
                         "purity", "maximum", "cluster_names", "purity")
walktrap_purity_plots

silhouette width plots

# Plot individual cluster and summary stats
walktrap_silhouette_plots <- plot_clustering_validity(walktrap_stats_df,
                         "width", "closest", "cluster_names", "silhouette")

walktrap_silhouette_plots

graph-based, louvain

# Check the louvain cluster validity stats for each of the clusters and return
# stats in a data frame
louvain_stats_df <- add_metadata_clustering_stats(sample_290_normalized, c(5, 10, 15, 20, 25), "louvain")

Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"

# Preview the results
head(louvain_stats_df)

# Summarize the stats and return in a data frame
louvain_summary_stats_df <- summarize_clustering_stats(louvain_stats_df)

# Preview the summary results
head(louvain_summary_stats_df)

purity plots

# Plot individual cluster and summary stats
louvain_purity_plots <- plot_clustering_validity(louvain_stats_df,
                         "purity", "maximum", "cluster_names", "purity")
louvain_purity_plots

silhouette width plots

# Plot individual cluster and summary stats
louvain_silhouette_plots <- plot_clustering_validity(louvain_stats_df,
                         "width", "closest", "cluster_names", "silhouette")
louvain_silhouette_plots

Check cluster stability

k-means

# Check and plot cluster stability
kmeans_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

graph-based, walktrap

walktrap_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

graph-based, louvain

louvain_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

Session info

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8    
 [5] LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
 [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] pheatmap_1.0.12             ggpubr_0.4.0                bluster_1.4.0              
 [4] readr_2.1.1                 scater_1.22.0               ggplot2_3.3.5              
 [7] scuttle_1.4.0               SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[10] Biobase_2.54.0              GenomicRanges_1.46.1        GenomeInfoDb_1.30.0        
[13] IRanges_2.28.0              S4Vectors_0.32.3            BiocGenerics_0.40.0        
[16] MatrixGenerics_1.6.0        matrixStats_0.61.0          magrittr_2.0.1             

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0          colorspace_2.0-2          ggsignif_0.6.3           
  [4] ellipsis_0.3.2            modeltools_0.2-23         rprojroot_2.0.2          
  [7] XVector_0.34.0            BiocNeighbors_1.12.0      rstudioapi_0.13          
 [10] farver_2.1.0              getopt_1.20.3             ggrepel_0.9.1            
 [13] flexmix_2.3-17            fansi_0.5.0               splines_4.1.2            
 [16] sparseMatrixStats_1.6.0   knitr_1.36                polyclip_1.10-0          
 [19] jsonlite_1.7.2            broom_0.7.10              cluster_2.1.2            
 [22] ggforce_0.3.3             BiocManager_1.30.16       compiler_4.1.2           
 [25] dqrng_0.3.0               backports_1.4.0           Matrix_1.3-4             
 [28] fastmap_1.1.0             cli_3.1.0                 limma_3.50.0             
 [31] tweenr_1.0.2              BiocSingular_1.10.0       miQC_1.2.0               
 [34] htmltools_0.5.2           tools_4.1.2               rsvd_1.0.5               
 [37] igraph_1.2.9              gtable_0.3.0              glue_1.5.1               
 [40] GenomeInfoDbData_1.2.7    dplyr_1.0.7               Rcpp_1.0.7               
 [43] carData_3.0-4             vctrs_0.3.8               DelayedMatrixStats_1.16.0
 [46] optparse_1.7.1            xfun_0.28                 stringr_1.4.0            
 [49] beachmat_2.10.0           lifecycle_1.0.1           irlba_2.3.3              
 [52] renv_0.14.0               statmod_1.4.36            rstatix_0.7.0            
 [55] edgeR_3.36.0              zlibbioc_1.40.0           MASS_7.3-54              
 [58] scales_1.1.1              hms_1.1.1                 parallel_4.1.2           
 [61] RColorBrewer_1.1-2        yaml_2.2.1                gridExtra_2.3            
 [64] stringi_1.7.6             ScaledMatrix_1.2.0        scran_1.22.1             
 [67] BiocParallel_1.28.2       rlang_0.4.12              pkgconfig_2.0.3          
 [70] bitops_1.0-7              evaluate_0.14             lattice_0.20-45          
 [73] purrr_0.3.4               labeling_0.4.2            cowplot_1.1.1            
 [76] tidyselect_1.1.1          here_1.0.1                R6_2.5.1                 
 [79] generics_0.1.1            metapod_1.2.0             DelayedArray_0.20.0      
 [82] pillar_1.6.4              withr_2.4.3               abind_1.4-5              
 [85] RCurl_1.98-1.5            nnet_7.3-16               tibble_3.1.6             
 [88] crayon_1.4.2              car_3.0-12                utf8_1.2.2               
 [91] tzdb_0.2.0                rmarkdown_2.11            viridis_0.6.2            
 [94] locfit_1.5-9.4            grid_4.1.2                digest_0.6.29            
 [97] tidyr_1.1.4               munsell_0.5.0             beeswarm_0.4.0           
[100] viridisLite_0.4.0         vipor_0.4.5